Linkage disequilibria and haplotype structure of four SNPs of the interleukin 1 gene cluster in seven Asian Indian populations

Variation at four single nucleotide polymorphism (SNP) sites of the interleukin 1 (IL1) gene cluster was investigated among 280 unrelated individuals, representing 7 caste groups from the state of Karnataka, India, and one European American community of Boston, Massachusetts. Allele and haplotype frequencies, strength of linkage disequilibrium, and signatures of recombination varied considerably among populations. Variable community sizes and traditions of consanguinity may account for the observed variation.     

LIF upregulates poFUT1 expression and promotes trophoblast cell migration and invasion at the fetal–maternal interface

Trophoblast cell migration and invasion are crucial for the establishment of a successful pregnancy. Protein O-fucosyltransferases, such as poFUT1 and poFUT2, catalyze the O-fucosylation of proteins and have important roles in embryonic development. Leukemia inhibitory factor (LIF) is a critical cytokine in the regulation of embryonic development and implantation. However, the exact roles of poFUTs in embryo migration and invasion and the effects of LIF on the expression of poFUTs have not been studied in detail. In the current study, we showed that poFUT1 and LIF were highly expressed in human trophoblast cells and in the serum of women during the first trimester of a normal pregnancy. However, in patients with threatened abortion, poFUT1 and LIF levels were found to be reduced. There were no significant differences in the expression levels of poFUT2 between the two groups. The migration and invasion potential of trophoblasts in an explant culture and in an in vitro implantation model was decreased or increased upon altering poFUT1 expression levels by siRNA or cDNA transfection. Our results also revealed that LIF upregulated the expression of poFUT1. The upregulation of poFUT1 by LIF promoted trophoblast cell migration and invasion at the fetal–maternal interface by activating the PI3K/Akt signaling pathway. Taken together, these study findings suggest that poFUT1 may be used as a marker of embryo implantation.Human pregnancy is a complex biological process that requires synchrony between the develop embryo and the receptive uterine endometrium. The fertilized egg divides into a 2-, 4-, and 8-cell embryo before developing into the morula and then into the mature blastocyst.^{1, 2} In the mature blastocysts, the inner cell mass (ICM), which comprises embryonic stem cells, differentiates into various tissues in the fetus. The trophoblast is the outer layer of embryonic tissue (also called villi) that facilitates the adhesion and penetration of the blastocysts into the endometrium during implantation. During the implantation of a human embryo, the progenitor trophoblast cells differentiate into the syncytiotrophoblast (STB) and the invasive trophoblast (iCTB) by different developmental pathways. The STB covers the villi and develops into the placenta, which mediates the exchange of nutrients, oxygen, and waste between maternal and fetal blood. The iCTB, which is derived from the trophoblast by epithelial–mesenchymal transition (EMT), forms cell columns and has a highly invasive character, causing it to migrate away from the attached embryo, invade the uterine epithelium and uterine spiral arteries to establish the maternal–fetal linkage.^{3, 4, 5, 6} However, poor iCTB migration and invasion often results in a failure to establish the maternal–fetal connection and leads to abortion. Many factors at the maternal–fetal interface, such as hormones (e.g., progesterone), growth factors and their receptors (e.g., EGF and EGFR), and cytokines (e.g., leukemia inhibitory factor (LIF)), regulate trophoblast invasion.^{7, 8, 9} These molecules increase the invasion potential of the embryo by increasing the expression levels of matrix metalloproteinases (MMPs) and decreasing that of the tissue inhibitor of MMP (TIMP).Protein glycosylation has an important role in many physiological and pathological processes, including inflammation, cancer metastasis, and embryo implantation.^{10, 11, 12} Protein fucosylation is one of the important types of glycosylation. It is classified into two kinds, N-fucosylation and O-fucosylation, which are catalyzed by fucosyltransferases (FUTs) and protein O-fucosyltransferases (poFUTs), respectively.^{13, 14} It is known that FUTs are expressed at specific stages of the menstrual cycle and are associated with reproductive function.^{15, 16} Ponnampalam et al.¹⁷ reported an increased expression level of FUT4 in the secretory phase as compared with that observed in the proliferative phase. We had previously shown that FUT4 and FUT7, which are expressed in uterine epithelial cells, influence the adhesion potential of the embryo.^{18, 19} poFUTs include poFUT1 and poFUT2. poFUT1 transfers L-fucose directly to the glycoproteins with epidermal growth factor (EGF)-like repeats.²⁰ A mutation in poFUT1 caused embryonic lethality in mice; silencing poFUT1 led to abnormal development in Drosophilas.^{20, 21} poFUT2 catalyzes the O-fucosylation of the glycoproteins with thrombospondin type 1 repeats (TSRs). The disruption of poFUT2 in mice resulted in teratomas.^{22, 23} However, the exact roles of poFUT1 and poFUT2 in human trophoblast migration and invasion have not been studied in detail.LIF, a pleiotropic cytokine of the interleukin-6 family, is essential for the successful completion of human pregnancy.^{24, 25} LIF, secreted by both the trophoblast and the uterine endometrium, mediates embryonic development and implantation in an autocrine or paracrine manner at the maternal–fetal interface. In the mother, LIF level peaks during the secretory/postovulatory phase of the menstrual cycle and regulates uterine receptivity for blastocyst implantation. In the fetus, LIF promotes trophoblast proliferation, invasion, and differentiation. Reduced expression level of LIF led to incomplete embryonic development. A deficiency of LIF results in implantation failure and causes repeated abortions or unexplained infertility.^{26, 27, 28, 29} However, the role of LIF-mediated regulation of poFUT1 and poFUT2 in embryo implantation has not been elucidated.In this study, we report that the levels of poFUT1 and LIF were higher in trophoblasts obtained from women with a normal pregnancy than those from patients with threatened abortion. However, the expression level of poFUT2 was not significantly different between the two groups. The poFUT1 promoted the migration and invasion of trophoblasts in an explant culture and in an in vitro implantation model. The upregulation of poFUT1 by LIF facilitated trophoblast cell migration and invasion through activating the PI3K/Akt signaling pathway.     

Oxidized phosphatidylcholine formation and action in oligodendrocytes

Reactive oxygen species play a major role in neurodegeneration. Increasing concentrations of peroxide induce neural cell death through activation of pro-apoptotic pathways. We now report that hydrogen peroxide generated sn-2 oxidized phosphatidylcholine (OxPC) in neonatal rat oligodendrocytes and that synthetic OxPC [1-palmitoyl-2-(5'-oxo)valeryl-sn-glycero-3 phosphorylcholine, POVPC] also induced apoptosis in neonatal rat oligodendrocytes. POVPC activated caspases 3 and 8, and neutral sphingomyelinase (NSMase) but not acid sphingomyelinase. Downstream pro-apoptotic pathways activated by POVPC treatment included the Jun N-terminal kinase proapoptotic cascade and the degradation of phospho-Akt. Activation of NSMase occurred within 1 h, was blocked by inhibitors of caspase 8, increased mainly C18 and C24:1 ceramides, and appeared to be concentrated in detergent-resistant microdomains (Rafts). We concluded that OxPC initially activated NSMase and converted sphingomyelin into ceramide to mediate a series of downstream pro-apoptotic events in oligodendrocytes.     

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

Current tools used in the reconstruction of ancestral gene orders often fall into event-based and adjacency-based methods according to the principles they follow. Event-based methods such as GRAPPA are very accurate but with extremely high complexity, while more recent methods based on gene adjacencies such as InferCARsPro is relatively faster, but often produces an excessive number of chromosomes. This issue is mitigated by newer methods such as GapAdj, however it sacrifices a considerable portion of accuracy. We recently developed an adjacency-based method in the probabilistic framework called PMAG to infer ancestral gene orders. PMAG relies on calculating the conditional probabilities of gene adjacencies that are found in the leaf genomes using the Bayes'' theorem. It uses a novel transition model which accounts for adjacency changes along the tree branches as well as a re-rooting procedure to prevent any information loss. In this paper, we improved PMAG with a new method to assemble gene adjacencies into valid gene orders, using an exact solver for traveling salesman problem (TSP) to maximize the overall conditional probabilities. We conducted a series of simulation experiments using a wide range of configurations. The first set of experiments was to verify the effectiveness of our strategy of using the better transition model and re-rooting the tree under the targeted ancestral genome. PMAG was then thoroughly compared in terms of three measurements with its four major competitors including InferCARsPro, GapAdj, GASTS and SCJ in order to assess their performances. According to the results, PMAG demonstrates superior performance in terms of adjacency, distance and assembly accuracies, and yet achieves comparable running time, even all TSP instances were solved exactly. PMAG is available for free at http://phylo.cse.sc.edu.